Evangelion: Broken Mirror
by shanejayell
Summary: In an alternate world there is a new leader for NERV....
1. Zero

Evangelion: Broken Mirror

Prologue: The Road Beyond Instrumentality

Gendo Ikari lowered the gun, watching Ritsuko Akagi fall dying to the floor, splashing in the LCL fluid spilling there. He felt a small flash of regret, more for what might have been than what he was doing, then the brown haired man turned away, knowing what he had to do.

Rei Ayanami waited there patiently, nude, gazing at him with empty eyes as the blue haired nude girl seemed to almost hang in mid air. Her red eyes seemed to peer right through Gendo, somehow, even though he knew that the only thing guiding her was the programing he implanted.

Pulling off his while gloves to reveal the Adam entity implanted in his palm Gendo stepped up only to freeze as Rei suddenly moved. Her hand shot up to grab him by the front of his Nerv uniform, holding him off easily.

"Rei...?" Gendo gasped.

"No," the eerily familiar voice said.

"Yui," Gendo's eyes went wide with a unholy combination of joy and fear.

Yui Ikari looked at him with a blank expression, but her true emotions swam in her startling red eyes. With a almost limitless contempt she asked, "Even with my soul in the Evangelion, did you not think I wouldn't be aware of what was going on?"

"I just wanted," Gendo said weakly, "you back."

"I went into Evangelion for a reason," Yui's voice was without mercy as she continued, "or did you just not care anymore?" Moving with a eerie sort of grace she took his hand in hers, then the Adam entity implanted there seemed to wiggle free, leaping to her as Gendo staggered away with a cry.

"Don't do this," Gendo begged, finally realizing what her intentions might be.

"Memory and consciousness is a strange thing," Yui looked down at her hands as the Adam entity flowed into her substance, "who knew that a few strands on RNA and DNA could hold so much? I remember it all, in this final moment."

"All?" Gendo felt his stomach drop.

"Naoko Akagi," Yui was coldly angry, "Ritsuko. The betrayal of my hopes and dreams, and the betrayal of everyone else."

"Please, Yui," Gendo begged from where he knelt in a puddle of LCL.

"It's over, Gendo," Yui turned away from him to where the Lilith entity was trapped on it's cross and floated towards it. There was but a moment's hesitation, then she seemed to flow into it like water.

"What have I done?" Gendo cluched his now Adam-less palm to his chest, his glasses half falling off his face.

Even as the Lilith entity shifted, it's body visibly reshaping itself, she tore free of the massive cross she was bound to, inhuman features rapidly becoming something much more pleasant. Absorbing any available LCL it shifted, growing and in a moment it had become a perfect replica of Yui, but on a immense scale.

"Goodbye, Gendo," Yui said as she seemed to ascend, rising towards the roof, "I'd wish you good luck, but there seems little point."

Ascending through NERV Yui got a sense of the chaos, seeing the United Nations forces battling against NERV troops and staff, the dead and dying. A rage kindled in her as she reached the surface, seeing first hand the actions of SEELE.

Asuka Soryu Langley's Unit 02 was torn to shreds, the pilot laying somewhere in the wreckage. The girl's mind was nearly broken from the trauma, only the last of her will keeping her from breaking down completely.

High up in the air Yui's son Shinji Ikari was trapped by the mass production models of Evangelion, his Unit 01 held captive like a fly in amber. Unlike the hardier Asuka he had finally broken, retreating from reality into a dream world of his own making.

Turning away from them Yui set to work, sending out pices of her spirit and essence out to the survivors. Ghost like these Rei copies passed through walls and obstacles, reaching each person and manifesting as their greatest wish or desire. As each individual fell they reverted to LCL, their souls freed for the next step.

Drawing from the earth the Egg of Lilith Yui drew the souls in even as she reached out to Unit 01 and the last part of herself. Taking that in she was whole for the first time in a age, cradling the now nearly catatonic Shinji in her hands. With a mixture of pity and tenderness she reduced him to LCL too, combining his soul with the rest of humanity.

This was it... the opportunity to return humanity to the Garden, to innocence... so why was she hesitating? Raising the Lilith Egg to her face she realized she could feel the souls within, and a few that cried out over the mass of humanity.

'This can't be the end,' Makoto Hyuuga struggled desperately.

'Sempai, I always wanted...,' Maya Ibuki grieved softly.

'I don't want to be alone,' Misato Katsuragi sounded fierce, 'but not like THIS.'

'I'm not giving up,' Shigeru Aoba fought on.

'Damn you, you are NOT hurting my sister,' Toji Suzuhara vowed.

Yui felt shock and even surprise as she turned the sphere of souls in her hands, hearing the voices of so many beings crying out against the unison. She had entered the Instrumentality project herself feeling that this was the best hope for all their children, that it could even be the begining of a new age.

Was she wrong?

Turning from those voices Yui Ikari reached out, seeking a certain voice and found only silence waiting for her. Shinji Ikari had simply pulled back into himself, torn away even from Instrumentality to hide away within the corridors of his own mind, the horrors that he had experienced too much for him.

"Oh my son," Yui murmured, "what have I done?"

'Then make it better, baka!' the voice demanded furiously.

'You?' Yui felt rather than saw the furious red-brown haired young woman, dressed in her red plugsuit.

Asuka Langley Soryu faced Yui directly, a mortal unaffraid in the face of something very like a god. 'I understand what's going on,' Asuka said defiantly, 'this... group mind-soup we're in told me that.'

'So what is going on, Asuka?" Yui challenged the younger woman.

'We can still go back,' Asuka said fiercely, 'the LCL is still there, we just need to put our wills into it. But first YOU have to let us go.'

'You have been hurt, betrayed, even killed by others, Asuka,' Yui mused, 'isn't this unity a better thing for all?'

'No,' Asuka said flatly.

'And why not?' Yui looked curious.

'A life without pain is death,' Asuka looked pained as she remembered her biological mother and added, 'or worse, insanity.' She seemed to take a breath, 'Even with the pain I've been through, the friendships make it worth it. Misato, that baka Toji, Hikaru even Shinji... I'm glad to have known them.'

'The world is in ruins,' Yui pointed out reasonably, yet still feeling the younger woman winning her over.

'I'd kind of think you could fix that, too,' Asuka noted, looking over the giant being, blazing with unearthly power.

Drawing her mind away from Asuka she looked across the now gutted wreckage of a world as Yui carefully weighed her words, as well as the wants of all those within the Egg of Lilith. Finally, it came down to humanity... the human soul within herself and the ones trapped inside the Egg. Raising the Egg of Lilith she focused her will and it seemed to almost explode as the souls within screamed free, racing back to their bodies.

"I don't have much time," Yui murmured.

Drawing on all her power the Yui/Lilith/Adam entity began to shrink, glowing brighter and brighter as energies built up within her. Weilding a power only slightly less than a god's Yui Ikari reached out, and the world...

...changed.

0o0o0o0o0o0o0

Yui Ikari awoke to the buzzing of her alarm, the light haired woman hitting it till it was silent. With a groan she got up, stumbling into the kitchen to start up the coffee. She frowned faintly, the fragments of a disturbing dream at the edges of her mind, but she dismissed it as nothing important.

To be continued...

Notes: Yui's consciousness only became active in the Rei body in Terminal Dogma with Gendo there. She was NOT having incestuous thoughts about Shinji throughout the TV series, tho BOY would that add a creepy little dynamic to the show.

"Hi, my name's Rei Ayanami. I am NOT your mother despite bearing a eerie resemblance to her and I am not thinking of having hot monkey-sex with my son."

Shinji, dumb as post, "Hi, nice to meet you."

lol This is, basically, a explanation for the AU universe of Broken Mirror and how it became so different than Eva. AS to why Yui would arrange that world in the way she did, consider that she had access to everyone's minds & souls while they were within the Egg of Lilith. That, and she might have wanted her own happy ending too.


	2. Chapter 1

Evangelion: Broken Mirror

Ritsuki Akagi intently studied the figure that was floating in the clear plastic tube, the blonde haired scientist frowning to herself slightly as she reviewed the data on display. Underneath her white lab coat she wore the form fitting uniform of a NERV officer, stone grey cloth trimmed in red, her stance and posture intent.

Within the clear plastic tube a young man floated fast asleep, light blue hair flowing around an average face. He was physically unremarkable, face unmarked by strain and almost unearthly in it's innocence. Designated Shinji Ayanami he was the greatest hope for NERV, and the weapon who would be pointed at the coming Angel threat.. at least hopefully.

The door to the chamber swished open and the leader of NERV walked up behind her, "How is the experiment going?"

Ritsuko turned around to look at Yui Ikari, meeting the gaze of the beautiful brown haired woman who was standing there. Like Ritsuko she too wore a labcoat but her uniform was colored dark blue, the insignia on her collar marking her as the commander of the underground facility of Tokyo-2. More importantly this project she commanded could very well be the final line of defence for humanity against a alien invasion.

"Not as well as we'd hoped," Ritsuko admitted. Gesturing towards Shinji she said, "We created him using genetic samples from your dead husband Gendo and the Adam entity, but our experiments show that he is limited in his ability to control Evanelion."

"We'll have to manage," Yui said quietly, "I have no wish to see ordinary children endangered in piloting Evangelion."

Ritsuko hesitated then she reached out a hand to rest on Yui's arm as she said seriously, "We may have no choice but to use the pilot trainees, Yui. I seriously doubt that a Shinji will be able to survive long fighting against the Angels."

Tensely Yui shrugged off the hand as she growled, "He'll have to." Without another word she strode out of the room, back stiff and steps fast.

Taken from the private journals of Yui Ikari:

Sometimes I hate my husband Gendo, even though he is long dead. Our expedition to investigate the Adam entity in Antarctica was peaceful, our plans perfect.. or at least that's what my arrogant spirit likes to believe. Somehow Gendo interfered with the Adam entity... and something catastrophic happened: Second Impact.

The research station was destroyed with nearly with all hands, the polar ice caps melted, and around the world humans died in mind boggling numbers. I still don't know who tossed Misato Katsuragi and myself into an escape capsule, both of us coming to rest on a island not far from the base. Frantically I fought to keep the badly injured Misato alive, staunching her blood flow and bandanging her chest wound even as tears flowed down my face...

"Commander," Misato called, the black haired young woman jogging up to her side. Unlike Yui she didn't wear a uniform, instead she was dressed in casual clothes with the rank insignia of a captain clipped onto her jacket.

"Misato," Yui smiled slightly as they fell into step together, looking at the young lady that she had nearly adopted. In the aftermath of Second Impact they had been thrown together by their mutual losses, developing a unlikely but strong bond.

"Are you looking forward to seeing your daughter?" Misato asked curiously, smiling up at the slightly taller Yui.

"Sort of," Yui admitted, smiling a bit grimly, "it's been months since I was able to visit Rei, but the idea of her coming here scares me."

Misato smiled at her, reaching out to gently squeeze her arm. "Rei wants to see her mom," she said to her softly, "understandably so. I know that your relatives have been taking care of her, but she must miss you."

They reached one of the elevators and went inside, each pressing a key for a different floor. "I wish I could get away from here to go see her," Yui closted her eyes a moment, rubbing at them tiredly, "but there's just no way."

"Well, would you feel a bit better if I went out to get her when she hits town?" Misato offered her help gently.

"I couldn't ask you..." Yui trailed off.

Misato chuckled softly, "You didn't ask, I offered." She smiled, "Rei is a good kid and we're friends. I'd be glad to help."

Yui gave her a lopsided grin, "Thanks." She gave her a mildly impish look, "Are you still seeing that ne'er do well, Kaji?"

"Yui!" Misato blushed faintly.

Yui looked amused, "I assume he must be good in the sack, considering he's lasted longer than most of your other boyfriends."

"Gah," Misato stepped out of the elevator fast once they reached her floor, her cheeks red. "I can't believe we're having this conversation," she shook her head grinning.

"See you later," Yui said as the door closed.

From the private journals of Yui Ikari:

In the aftermath of Second Impact I could barely look at little Rei, now barely a few weeks old. Her black hair reminded me so much of her father Gendo, but her eyes were purely innocent in a way that his had never been. She helped pull me through all the pain and grief I felt due to my role in Second Impact, spending my time with her and Misato even as I opened up negotiations with the United Nations.

It was clear to everyone that if there was a Third Impact humanity wouldn't survive, and so NERV was founded to research the earlier Impacts and attempt to prepare a possible defence. In studying Adam and other sources I created the biomechanical being Evangelion... in some ways a complete perversion of my earlier work. I dreamed of healing the body with synthetic parts, but instead I have created a engine of destruction.

Making things more complicated has been the discovery of encrypted files belongig to Gendo detailing his involvement with something called SEELE. At the very least they were aware of both Adam and our expedition to contact it, and possibly they may have even financed our trip. If it's true they may have played a hand in Gendo triggering Second Impact, and hints in the documents indicate they might be pulling strings in governments around the world...

In her office later that day Yui closed the data file, silently musing on all the twists that had come to her life. The sound of a chime got her attention away from her journal and she closed the file as Yui called out, "Come in."

Maya Ibuki nodded respectfully as the young officer set her report on the table. Her black hair fell into her eyes as she reported formally, "The command center is fully online, ma'am, and the city defences report fully operational."

'She's so formal,' Yui noted. "Thank you, Maya," she said as she took the documents, "you've done excelent work."

"Ritsuko-sempai did the difficult work," Maya's eyes nearly shone, "completing the computer integration with the Magi."

Yui fought back her amusement at the young lady's hero worship as she agreed, "Yes, Ritsuko really is something." She studied Maya a moment, "As you know, we're going to need reliable officers in the comand center when the Angels attack... would you be interested in such a position?"

Maya saluted, "Ma'am, I'd be honored."

'Especially since it means you'll be working closely with Ritsuko,' Yui thought impishly. "The with your permission we'll switch you over from technical services," she stood to shake the girl's hand, "welcome aboard."

"Ma'am," Maya nodded happily, clearly fighting back a skip in her step as she left.

A few moments later the door swished open once again and Yui smiled faintly as her guest came inside. "I'm sorry for being so short with you this morning," she apologized, getting up from behind her desk.

"It's all right," Ritsuko smiled as she took Yui's hand and squeezed it gently, "I understand. You wouldn't be the person you are if you didn't want to keep anyone else from being hurt."

"Thank you," Yui delicately took Ritsuko's hand in both of hers. She smiled slightly as she met Ritsuko's eyes, " I think Maya has a crush on you."

Ritsuko stepped closer, her eyes gently amused. "I noticed," she admitted as shestood bare inches from Yui, "I'm trying to let her down gently."

Yui swallowed, her breath coming a little faster. "Ritsuko...," she started.

"Hush," Ritsuko leaned forward, closing the distance to press her lips to Yui's, slinding her free hand behind the other woman's head.

Yui moaned as they drew apart a bit, her own hands having slipped free from Ritsuko's to slide around the other woman's body. "I'm your commanding officer," Yui sighed, "we shouldn't be doing this."

"I'm a grown woman," Ritsuko said, keeping a firm grip on Yui, "and I was the one who approached you, remember?"

"That doesn't excuse me," Yui sighed.

Ritsuko smirked, "I wasn't looking for excuses." And with that she gently pulled her into a kiss once again.

End.

Notes: This was inspired by a comment that there weren't enough Yui Ikari fics, so I decided to try to write one. The premise is an alternate EVA where Gendo died instead of Yui, and it looks at the way things might have gone afterward. I've left this deliberately open ended so that I or other authors could continue it later...


End file.
